Synteny Analysis - Usage Guide

Overview

Synteny analysis detects conserved gene order across genomes and identifies structural rearrangements. MCScanX (Wang 2012) is the most widely used dynamic-programming tool for collinear gene blocks. JCVI / MCScan Python (Tang 2008) provides publication-grade visualization. GENESPACE (Lovell 2022) is the modern standard for plant comparative genomics with riparian plots and pan-gene tracks. SyRI (Goel 2019) handles structural variant detection from whole-genome alignment.

The fundamental distinction: synteny != collinearity (synteny is "same chromosome"; collinearity is "same order"). The choice of tool depends on whether the question is gene-level co-linearity (MCScanX, JCVI), whole-genome structural rearrangements (SyRI, AnchorWave), multi-genome macrosynteny (GENESPACE, ntSynt), or synteny-aware orthology (GENESPACE, ProteinOrtho-synteny).

For whole-genome alignment substrate (Cactus / Minigraph-Cactus), see [[whole-genome-alignment]]. For WGD-aware analysis (Ks plots), see [[whole-genome-duplication]]. For pangenome graphs, see [[pangenome-analysis]].

Prerequisites

# MCScanX (compile from source)
git clone https://github.com/wyp1125/MCScanX && cd MCScanX && make

# JCVI / MCScan Python
pip install jcvi

# GENESPACE (R)
Rscript -e "remotes::install_github('jtlovell/GENESPACE')"
# GENESPACE bundles OrthoFinder 2.5.x specifically

# SyRI + plotsr
conda install -c bioconda syri plotsr

# AnchorWave (WGD-aware)
conda install -c bioconda anchorwave

# i-ADHoRe 3.0 (deeply diverged species)
git clone https://github.com/VIB-PSB/i-ADHoRe && cd i-ADHoRe && mkdir build && cd build && cmake .. && make

# ntSynt (multi-genome macrosynteny)
pip install ntsynt

# Pairwise WGA tools
conda install -c bioconda minimap2 mummer4

# Repeat masking (MANDATORY before synteny)
conda install -c bioconda repeatmodeler repeatmasker

Quick Start

Tell the AI agent what to do: - "Detect syntenic blocks between two plant genomes using MCScanX" - "Build a riparian plot of synteny across 10 grass genomes with GENESPACE" - "Find structural rearrangements (inversions, translocations, duplications) with SyRI" - "Generate publication-grade dotplot with JCVI for human vs mouse synteny"

Example Prompts

Plant Comparative Genomics

"Compare Arabidopsis thaliana, Brassica napus, Camelina sativa, and Capsella rubella using GENESPACE. Build the riparian plot with orthogroup-constrained anchors. Identify lineage-specific gene gains and losses via pan-gene tracks. Cross-reference with [[whole-genome-duplication]] for WGD context."

Structural Variant Inventory

"Identify INVs, TRANSs, and DUPs between two Solanum lycopersicum cultivars using minimap2 -x asm5 + SyRI + plotsr. Filter SyRI INVs to > 5 kb (biological-relevance threshold). Cross-validate with PacBio long-read SV calls."

Microsynteny Network Analysis

"Build a synteny network across 50 angiosperm genomes using SynNet. Identify microsynteny-conserved gene clusters (metabolic operons, NLR clusters) that persist across deep divergence. Compare with macrosynteny decay."

What the Agent Will Do

1. Validate inputs: assembly N50 (>= 1 Mb); BUSCO/Compleasm completeness; repeat masking
2. Pre-mask repeats: RepeatModeler2 species-specific library + RepeatMasker softmask
3. All-vs-all BLAST: DIAMOND (faster) or BLASTP+
4. Run synteny detection with appropriate tool:
5. MCScanX for general use
6. GENESPACE for plant comparative
7. JCVI for publication plots
8. SyRI for structural variants
9. AnchorWave for WGD lineages
10. Tandem duplicate collapse: automatic in MCScanX (5-gene window default)
11. Classify synteny relationships: 1:1, 1:many, many:many
12. For SVs: minimap2 + SyRI; filter INVs > 5 kb
13. Visualize: dotplots, karyotypes, riparian plots, plotsr SV plots
14. Cross-validate: MCScanX vs JCVI (consistent stringency)
15. Report: block-level statistics, synteny scale (micro vs macro), per-chromosome relationships
16. Caveats: repeat-driven false synteny, fragmentation, tandem inflation, reference-guided bias, WGD effects

Tips

• Soft-mask repeats before BLAST; unmasked TEs produce millions of paralogous hits
• Minimum N50 of 1 Mb for reliable synteny detection
• Reference-guided scaffolding creates circular reasoning if used for self-comparison
• MCScanX block size minimum: -s 5 (5 anchor genes); raise to 10 for stringent
• GENESPACE is the modern standard for plant comparative; OrthoFinder + MCScanX-constrained
• For animal/fungal multi-genome, JCVI is most generally useful
• SyRI requires chromosome-level assemblies; works on pairs
• AnchorWave WGD-aware proali mode requires explicit ploidy
• For deeply diverged species (< 70% identity), i-ADHoRe or LASTZ chains/nets
• minimap2 -x asm5 for closely related; LASTZ for distant
• ntSynt for alignment-free multi-genome macrosynteny
• For Ks-dating of synteny blocks, see [[whole-genome-duplication]]
• Tandem duplicates collapsed by MCScanX 5-gene window default; tune for NLR clusters
• Microsynteny vs macrosynteny: minimum 5 anchors microsynteny; 20+ macrosynteny
• For WGA substrate at clade level, see [[whole-genome-alignment]]
• Document microsynteny vs macrosynteny scale in any synteny claim

Related Skills

comparative-genomics/whole-genome-duplication - Ks-based WGD detection, KsRates comparative-genomics/whole-genome-alignment - Cactus / Minigraph-Cactus / LASTZ comparative-genomics/ortholog-inference - GENESPACE depends on OrthoFinder comparative-genomics/pangenome-analysis - Bacterial pangenome (different problem) comparative-genomics/comparative-annotation-projection - TOGA / CESAR via WGA-derived synteny comparative-genomics/positive-selection - Selection on syntenic gene pairs phylogenetics/modern-tree-inference - Phylogenetic context for dating genome-assembly/assembly-qc - BUSCO before synteny alignment/structural-alignment - Sequence-level underlying SyRI variant-calling/structural-variant-calling - Short-read SV (orthogonal to SyRI WGA)